Man pages for jefferis/nat
NeuroAnatomy Toolbox for Analysis of 3D Image Data

affmat2cmtkparamsDecompose homogeneous affine matrix to CMTK registration...
all.equal.dotpropsall.equal method tailored to dotprops objects
all.equal.im3dCheck equality on data and key attributes of im3d objects
all.equal.neuronCheck equality on key fields of neuron object
amiramesh-ioRead AmiraMesh data in binary or ascii format
amiratypeReturn the type of an amiramesh file on disk or a parsed...
as.hxsurfConvert an object to a nat hxsurf object
as.im3dConvert a suitable object to an im3d object.
as.mesh3dConvert an object to an rgl mesh3d
as.neuronlistMake a list of neurons that can be used for coordinate...
as.neuronlist.neuronlistfhconvert neuronlistfh to a regular (in memory) neuronlist
boundingboxGet the bounding box of an image volume or object containing...
Cell07PNsCell07PNs: 40 Sample Projection Neurons from Jefferis, Potter...
clampmaxReturn function that finds maximum of its inputs within a...
cmtk.bindirReturn path to directory containing CMTK binaries
cmtk.callUtility function to create and run calls to CMTK commandline...
cmtk.dof2matConvert CMTK registration to homogeneous affine matrix with...
cmtk.extract_affineExtract affine registration from CMTK registration file or...
cmtk.mat2dofUse CMTK mat2dof to convert homogeneous affine matrix into...
cmtkparams2affmatCompose homogeneous affine matrix from CMTK registration...
cmtk.reformatxReformat an image with a CMTK registration using the...
cmtkregCreate and test cmtkreg objects that specify path to a CMTK...
cmtkreglistMake in-memory CMTK registration list from affine matrix or...
cmtk.statisticsCalculate image statistics for a nrrd or other CMTK...
cmtk.targetvolumeDefines a target volume for a CMTK reformatx operation
cmtk.versionReturn cmtk version or test for presence of at least a...
c.neuronlistCombine multiple neuronlists into a single list
coord2indFind 1D indices into a 3D image given spatial coordinates
dotpropsdotprops: Neurons as point clouds with tangent vectors (but...
dotprops-arithmeticArithmetic for nat dotprops and surface objects
fileformatsSet or return list of registered file formats that we can...
find.neuronFind neurons within a 3D selection box (usually drawn in rgl...
find.somaFind neurons with soma inside 3D selection box (usually drawn...
flipFlip an array, matrix or vector about an axis
get-set-neuronlist-data.frameGet or set the attached data.frame of a neuronlist
graph.nodesReturn root, end, or branchpoints of an igraph object
im3dConstruct an im3d object representing 3D image data,...
im3d-coordsInterconvert pixel and physical coordinates
im3d-ioRead/Write calibrated 3D blocks of image data
image.im3dMethod to plot spatially calibrated image arrays
imexpand.gridConvert locations of im3d voxel grid into XYZ coordinates
imscalebarMake a scalebar to accompany an image.im3d plot
imsliceSlice out a 3D subarray (or 2d matrix) from a 3D image array
ind2coordFind XYZ coords corresponding to 1D indices into a 3D image
intersectFind the intersection of two collections of objects
intersect_planeFind the points on a plane that are intersected by an object
is.amirameshCheck if file is amiramesh format
is.fijitracesCheck whether a file is in Fiji's simple neurite tracer...
is.im3dTest if an object is of class im3d
is.neuromlCheck whether a file is in NeuroML format
is.neuronlistTest objects of neuronlist class to store multiple neurons
is.nrrdCheck if a file is a NRRD file
is.swcTest if a file is an SWC format neuron
is.vaa3drawCheck if a file is in the raw image format used by Hanchuan...
kcs20List of 20 Kenyon Cells from Chiang et al 2011 converted to...
makeboundingboxConstruct a 3D bounding box object
maskMask an object, typically to produce a copy with some values...
materialsExtract or set the materials for an object
MBL.surfSurface object (hxsurf) for the left mushroom body in FCWB...
mirrorMirror 3D object about a given axis, optionally using a...
nat-packageAnalyse 3D biological image data especially neurons
ndigestCalculated normalised digest value for an object
neuronneuron: class to represent traced neurons
neuron-arithmeticArithmetic for neuron coordinates
neuronlistCreate a neuronlist from zero or more neurons
neuronlist-arithmeticArithmetic for neuron coordinates applied to neuronlists
neuronlist-dataframe-methodsMethods for working with the dataframe attached to a...
neuronlistfhneuronlistfh - List of neurons loaded on demand from disk or...
ngraphngraph: a graph to encode a neuron's connectivity
nlapplylapply and mapply for neuronlists (with optional...
nlscanScan through a set of neurons, individually plotting each one...
nopen3dOpen customised rgl window
normalise_swcNormalise an SWC format block of neuron morphology data
npop3dRemove plotted neurons or other 3D objects
nrrd.voxdimsReturn voxel dimensions (by default absolute voxel...
nverticesFind the number of vertices in an object (or each element of...
nview3dSet the 3D viewpoint of an RGL window using anatomical terms
originReturn the space origin of a 3D image object
pan3dSome useful extensions / changes to rgl defaults
plane_coefficientsFind the coefficients of the plane equation
plot3dplot3d methods for different nat objects
plot3d.boundingboxPlot a bounding box in 3D
plot3d.cmtkregPlot the domain of a CMTK registration
plot3d.dotprops3D plots of dotprops objects using rgl package
plot3d.hxsurfPlot amira surface objects in 3D using rgl
plot3d.neuronPlot neurons in 3D using rgl library
plot3d.neuronlist3D plots of the elements in a neuronlist, optionally using a...
plot.neuronPlot a 2D projection of a neuron
plot.neuronlist2D plots of the elements in a neuronlist, optionally using a...
pointsinsideFind which points of an object are inside a surface
potential_synapsesCalculate number of potential synapses between two neurons
projectionMake 2D (orthogonal) projection of 3D image data
pruneprune an object by removing points near (or far) from a...
prune_strahlerPrune a neuron by removing segments with a given Strahler...
prune_verticesPrune selected vertices or edges from a neuron
read.cmtkRead CMTK TypedStream file to a list in memory
read.cmtkregRead a CMTK format registration
read.hxsurfRead Amira surface (aka HxSurface or HyperSurface) files into...
read.landmarksGeneric functions to read/write landmarks in any supported...
read.morphmlReturn parsed XML or R list versions of a NeuroML file
read.neuronRead a single neuron from a file
read.neuron.fijiRead a neuron saved by Fiji's Simple Neurite Tracer Plugin
read.neuronlistfhRead a local, or remote, neuronlistfh object saved to a file.
read.neuron.neuromlRead one or more neurons from a NeuroML v1 file
read.neuronsRead one or more neurons from file to a neuronlist in memory
read.neuron.swcRead a neuron in swc file format
read.nrrdRead NRRD files/headers into memory
read.vaa3drawRead Vaa3d format image data
reglistA simple wrapper class for multiple transformations
remotesyncSynchronise a remote object
resampleResample an object with a new spacing
rootpointsReturn the root, branch, or end points of a neuron or graph
scale.neuronScale and centre neuron 3D coordinates
seglengthsCalculate length of all segments in neuron
seglistMake/convert neuron connectivity information into a seglist...
seglist2swcRecalculate Neurons's SWCData using SegList and point...
segmentgraphReturn a simplified segment graph for a neuron
setdiffFind the (asymmetric) difference between two collections of...
simplify_reglistSimplify a registration list
smooth_neuronSmooth the 3D coordinates of a neuron skeleton
spineCompute the longest path (aka spine or backbone) of a neuron
strahler_orderFind the Strahler order of each point in a neuron
sub2indFind 1D index given n-dimensional indices
sub-.neuronlistfhExtract from neuronlistfh object or its attached data.frame
subsetSubset methods for different nat objects
subset.dotpropsSubset points in dotprops object that match given conditions
subset.hxsurfSubset hxsurf object to specified regions
subset.neuronSubset neuron by keeping only vertices that match given...
subset.neuronlistSubset neuronlist returning either new neuronlist or names of...
summary.neuronSummary statistics for neurons (e.g. cable length, number of...
thresholdThreshold an object, typically to produce a mask
unionFind the union of two collections of objects
unmaskMake im3d image array containing values at locations defined...
voxdimsReturn voxel dimensions of an object
write.amirameshWrite a 3D data object to an amiramesh format file
write.cmtkWrite a suitable list to a CMTK TypedStream file on disk
write.cmtkregWrite out CMTK registration list to folder
write.hxsurfWrite Amira surface (aka HxSurface or HyperSurface) into...
write.neuronWrite out a neuron in any of the file formats we know about
write.neuronlistfhWrite out a neuronlistfh object to an RDS file
write.neuronsWrite neurons from a neuronlist object to individual files,...
write.nrrdWrite data and metadata to NRRD file or create a detached...
write.vtkWrite object to VTK file
xformTransform the 3D location of objects such as neurons
xformimageTransform image files using a registration or affine matrix
xformpointsTransform 3D points using a registration, affine matrix or...
xyzmatrixGet and assign coordinates for classes containing 3D vertex...
jefferis/nat documentation built on Oct. 25, 2018, 6:29 p.m.